Salvelinus alpinus

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Resource Primary Assembly Alternate Assembly
GenBank fSalAlp2: GCA_036784965.1 fSalAlp2: GCA_036784925.1
ENA fSalAlp2: GCA_036784965.1 fSalAlp2: GCA_036784925.1
UCSC Genome Browser fSalAlp2: GCA_036784965.1 fSalAlp2: GCA_036784925.1

No image
Raw Data by Technology
Datatype Individual Bases Coverage Bytes Access
PacBio HiFi (.fq) fSalAlp3 104.20 Gbp N/A 61.6 GiB
PacBio HiFi (.bam) fSalAlp3 100.73 Gbp N/A 382.9 GiB
Arima fSalAlp3 238.05 Gbp N/A 121.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 December 2025.
Raw Data by Individual
Individual Datatype Bases Coverage Bytes Access
fSalAlp3 PacBio HiFi (.fq) 104.20 Gbp N/A 61.6 GiB
PacBio HiFi (.bam) 100.73 Gbp N/A 382.9 GiB
Arima 238.05 Gbp N/A 121.1 GiB
Bases and Coverage are approximate.
Coverage based on genome size .
Last upload on 8 December 2025.
Assemblies
Individual 3 Haplotype 1 Assembly
Version assembly_curated from 3 December 2025
fSalAlp3.hap1.cur.20251203.fasta.gz (515.7 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 41 4.32 Mbp 3 81.29 Mbp
20 107 2.84 Mbp 6 64.54 Mbp
30 201 2.03 Mbp 9 62.22 Mbp
40 334 1.45 Mbp 13 55.87 Mbp
50 523 1.01 Mbp 17 53.65 Mbp
60 791 0.72 Mbp 22 49.16 Mbp
70 1169 499.97 Kbp 26 45.93 Mbp
80 1742 314.69 Kbp 32 42.43 Mbp
90 2742 160.39 Kbp 37 36.39 Mbp
100 5883 10.18 Kbp 1442 10.18 Kbp
1.000x 5883 2.26 Gbp 1442 2.26 Gbp
NG based on genome size .
Individual 3 Haplotype 2 Assembly
Version assembly_curated from 3 December 2025
fSalAlp3.hap2.cur.20251203.fasta.gz (470.0 MiB)

Quality: not computed

Contigs Scaffolds
NG LG Len LG Len
10 40 3.90 Mbp 3 70.31 Mbp
20 105 2.56 Mbp 6 57.23 Mbp
30 196 1.90 Mbp 9 52.95 Mbp
40 322 1.34 Mbp 13 50.33 Mbp
50 503 0.91 Mbp 17 46.68 Mbp
60 770 0.62 Mbp 22 42.16 Mbp
70 1170 409.76 Kbp 27 39.93 Mbp
80 1790 259.73 Kbp 32 35.28 Mbp
90 2856 129.88 Kbp 38 28.42 Mbp
100 6083 10.27 Kbp 1796 10.27 Kbp
1.000x 6083 2.01 Gbp 1796 2.01 Gbp
NG based on genome size .
Individual 3 Mitochondrial Assembly
Version assembly_MT_rockefeller from 14 September 2023
fSalAlp3.MT.20230914.fasta.gz (5.4 KiB)

Quality: not computed
Assembly Metadata
assembly_vgp_HiC_2.0/fSalAlp3_hap1.yml (view)
species: Salvelinus alpinus
specimen: fSalAlp3
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap1
hap1: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/fSalAlp3.HiC.hap1.20230829.fasta.gz
hap2: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/fSalAlp3.HiC.hap2.20230829.fasta.gz
pretext_hap1: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fSalAlp3_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fSalAlp3_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/merqury/fSalAlp3_png/
pacbio_read_dir: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/genomic_data/arima/
mito: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_MT_rockefeller/fSalAlp3.MT.20230914.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fSalAlp3, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT. 
assembly_vgp_HiC_2.0/fSalAlp3_hap2.yml (view)
species: Salvelinus alpinus
specimen: fSalAlp3
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/fSalAlp3.HiC.hap1.20230913.fasta.gz
hap2: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/fSalAlp3.HiC.hap2.20230913.fasta.gz
pretext_hap1: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fSalAlp3_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fSalAlp3_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/merqury/fSalAlp3_png/
pacbio_read_dir: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/genomic_data/arima/
mito: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_MT_rockefeller/fSalAlp3.MT.20230913.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fSalAlp3, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT. 

species: Salvelinus alpinus
specimen: fSalAlp3
projects: 
  - vgp
assembled_by_group: Rockefeller
data_location: S3
release_to: S3
haplotype_to_curate: hap2
hap1: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/fSalAlp3.HiC.hap1.20230829.fasta.gz
hap2: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/fSalAlp3.HiC.hap2.20230829.fasta.gz
pretext_hap1: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/hap1/pretext/fSalAlp3_hap1_s2.pretext
pretext_hap2: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/hap2/pretext/fSalAlp3_hap2_s2.pretext
kmer_spectra_img: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_vgp_HiC_2.0/evaluation/merqury/fSalAlp3_png/
pacbio_read_dir: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/genomic_data/pacbio_hifi/
pacbio_read_type: hifi
hic_read_dir: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/genomic_data/arima/
mito: s3://genomeark/species/Salvelinus_alpinus/fSalAlp3/assembly_MT_rockefeller/fSalAlp3.MT.20230914.fasta.gz
pipeline: 
  - hifiasm (0.19.3+galaxy0)
  - purge_dups
  - yahs (1.2a.2+galaxy1)
notes: This was a Hifiasm-HiC assembly of fSalAlp3, resulting in two complete haplotypes. HiC scaffolding was performed with YaHS.  The HiC prep kit used was Swift-IDT. 
Data Use Policy

Samples and data come from a variety of sources. To support fair and productive use of this data, please abide by the Data Use Policy and contact Erich D. Jarvis, ejarvis@rockefeller.edu, with any questions.